Watching DNA polymerase η make a phosphodiester bond

Native human DNA polymerase η, DNA and dATP were crystallized at pH 6.0 without Mg(2+). The polymerization reaction was initiated by exposing crystals to 1 mM Mg(2+) at pH 7.0, and stopped at various time points by freezing at 77 K for crystallographic analysis. The substrates and two Mg(2+) are aligned for reaction within 40 seconds, but the new bond begins to form at 80 seconds. Structures at reaction times from 80s to 300s reveal a mixture of decreasing substrate and increasing product of the nucleotidyl-transfer reaction. In sequence, the nucleophile 3′-OH is deprotonated, the deoxyribose at the primer end converts from C2′-endo to C3′-endo to avoid steric clashes, and the nucleophile and the α-phosphate of dATP approach each other to form the new bond. A third Mg(2+) ion, which arrives with the new bond and stabilizes the intermediate state, may be an unappreciated feature of the two-metal-ion mechanism.